Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived neural crests
NA
NA

Attributes by original data submitter

Sample

source_name
Cranial neural crest cells
individual
3
cell type
Cranial neural crest cells (CNCCs)
cnccs derived from
WT33 iPSC
chip antibody
anti-H3K4me3 (Active Motif, catalog# 39159, lot# 12613005)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIPs were performed using approximately 0.5-1 x 10^7 CNCCs fixed with 1% formaldehyde for 10 min at room temp. RNA was extracted using Trizol. Sequencing libraries were prepared starting from ~30ng of ChIP DNA or oligo-dT purified mRNA using the NEBNext Multiplex Oligos for Illumina kit (Cat# E7335S).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
29521560
Reads aligned (%)
91.8
Duplicates removed (%)
24.5
Number of peaks
25683 (qval < 1E-05)

hg19

Number of total reads
29521560
Reads aligned (%)
91.6
Duplicates removed (%)
24.7
Number of peaks
25722 (qval < 1E-05)

Base call quality data from DBCLS SRA